Unlocking the Great Bay Temple in Majora’s Mask does not necessarily have to be done within a single three-day cycle. The temple can be accessed and explored at any time after the player has obtained the Zora Mask and has made their way to the Great Bay area. However, completing the temple and obtaining all its items, including the Boss Key, may require some progression through the game’s storyline and the collection of specific items and masks.

Here is a step-by-step guide to help you unlock and navigate the Great Bay Temple:

1. **Obtain the Zora Mask**:
– To access the Great Bay Temple, you need to have the Zora Mask. This mask allows you to swim and interact with underwater environments.

2. **Reach Great Bay**:
– Use the Great Bay Turtle to reach the temple. The turtle will take you to the foggy landmass that is Great Bay Temple.

3. **Enter the Temple**:
– After reaching Great Bay, head straight up the ramp through the first door. This will lead you into the temple.

4. **Light the Torches**:
– Before proceeding, light all the torches in the first room to make a Stray Fairy appear.

5. **Navigate the First Room**:
– Pull out your bow and snipe the Skulltula to the left, high above, then grab another Stray Fairy. Put on the Zora mask and swim to the far right corner of the room to find a crank. Push it to make a waterspout appear that creates a bridge to cross the gap on the upper level.

6. **Retrieve Stray Fairies**:
– Continue to retrieve more Stray Fairies by breaking pots and barrels using the Zora boomerangs and diving underwater.

7. **Defeat the Mini-Boss (Wart)**:
– Enter the room with the Wart and use your hookshot or arrows to pull the pink eyes away from the center mass. Shoot the eye when you have a clear path to it. After three hits, the rest of the eyes will drop off, and you can slash through them with your sword. Two hits on the Wart’s eye will defeat it, and you will receive the Ice Arrows.

8. **Follow the Red Pipeline**:
– Dive down off the platform and use the Zora Mask to dive down. Follow the red pipeline through the dungeon, ensuring the water flows back to the waterwheel early on. This will help you navigate through various passageways.

9. **Obtain the Boss Key**:
– Follow the red pipeline backward, passing through rooms with Bio Deku Babas and Dexihands. Use Ice Arrows to create a path to a blue passageway with icicles on the floor. Swim up onto the ice block and jump to the ledge. This will lead you to the Boss Key.

10. **Navigate to the Boss Room**:
– From the turbine room, look for a passageway with a single green pipe leading into it. This will take you to the boss room.

11. **Complete Any Remaining Tasks**:
– Ensure all stray fairies are collected and any other items or side quests are completed before leaving the temple.

By following these steps, you can unlock and navigate the Great Bay Temple without being confined to a single three-day cycle. However, some progression through the game’s storyline and item collection may be necessary to fully explore and complete the temple.